chrX-85095004-A-T

Variant names:

• chrX-85095004-A-T
• rs4828326
• NM_001367857.2:c.1694-8T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367857.2(SATL1):​c.1694-8T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: SATL1 NM_001367857.2 splice_region, intron
• Scores: Splicing: ADA: 0.2585
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 9 publications found

Genes affected

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367857.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	NM_001367857.2	MANE Select	c.1694-8T>A		splice_region intron	N/A	NP_001354786.1	Q86VE3-1
	SATL1	NM_001367858.2		c.1694-8T>A		splice_region intron	N/A	NP_001354787.1	A0A2R8YFQ0
	SATL1	NM_001012980.2		c.1694-8T>A		splice_region intron	N/A	NP_001012998.2	Q86VE3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	ENST00000644105.2	MANE Select	c.1694-8T>A		splice_region intron	N/A	ENSP00000494345.1	Q86VE3-1
	SATL1	ENST00000509231.1	TSL:1	c.1694-8T>A		splice_region intron	N/A	ENSP00000425421.1	Q86VE3-2
	SATL1	ENST00000646118.1		c.1694-8T>A		splice_region intron	N/A	ENSP00000493598.1	Q86VE3-1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 934296 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 265042

African (AFR) AF: 0.00 AC: 0 AN: 23466

American (AMR) AF: 0.00 AC: 0 AN: 33905

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17858

East Asian (EAS) AF: 0.00 AC: 0 AN: 29320

South Asian (SAS) AF: 0.00 AC: 0 AN: 48802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3776

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 697327

Other (OTH) AF: 0.00 AC: 0 AN: 40418

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		0.39

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.26
dbscSNV1_RF	Benign	0.38
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4828326; hg19: chrX-84350010;